R/gtoxLoadUnit.R

In GladiaTOX: R Package for Processing High Content Screening data

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#-------------------------------------------------------------------------------
# gtoxLoadUnit: Load response units for assay endpoints
#-------------------------------------------------------------------------------

#' @title Load response units for assay endpoints
#'
#' @description
#' \code{gtoxLoadUnit} queries the gtox databases and returns a data.table
#' with the response units for the given assay endpoint ids (aeid).
#'
#' @param aeid Integer, assay endpoint ids
#'
#' @keywords internal
#' 
#' @return A data.table containing level 3 correction methods for the given
#' aeids.
#'
#' @seealso \code{\link{gtoxQuery}}, \code{\link{data.table}}
#'
#' @import data.table

gtoxLoadUnit <- function(aeid) {

    qformat <-
        "
        SELECT
            aeid,
            normalized_data_type AS resp_unit
        FROM
            assay_component_endpoint
        WHERE
            aeid IN (%s);
        "

    qstring <- sprintf(qformat, paste(aeid, collapse=","))

    dat <- gtoxQuery(query=qstring, db=getOption("TCPL_DB"))

    if (nrow(dat) == 0) {
        warning("The given aeid(s) do not have response units.")
        return(dat)
    }

    len_miss <- lw(!aeid %in% dat$aeid)
    if (len_miss > 0) {
        warning(len_miss, "of the given aeid(s) do not have response units.")
    }

    dat[]

}

#-------------------------------------------------------------------------------